Single Site class.

disorderedmaterials · Nov 13, 2024 · f7386ae · f7386ae
1 parent 5ef24f8
commit f7386ae
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Showing 12 changed files with 53 additions and 106 deletions.
diff --git a/src/classes/site.cpp b/src/classes/site.cpp
@@ -6,17 +6,23 @@
 #include "base/messenger.h"
 #include <utility>
 
-/*
- * Site
- */
-
 Site::Site(const SpeciesSite *parent, std::optional<int> uniqueSiteIndex, std::shared_ptr<const Molecule> molecule,
            const Vec3<double> &origin)
+    : parent_(parent), uniqueSiteIndex_(uniqueSiteIndex), molecule_(std::move(molecule)), origin_(origin)
+{
+}
+
+Site::Site(const SpeciesSite *parent, std::optional<int> uniqueSiteIndex, std::shared_ptr<const Molecule> molecule,
+           const Matrix3 &axes, const Vec3<double> &origin)
+    : parent_(parent), uniqueSiteIndex_(uniqueSiteIndex), molecule_(std::move(molecule)), origin_(origin), axes_(axes),
+      hasAxes_(true)
+{
+}
+
+// Return enum options for SiteAxis
+EnumOptions<Site::SiteAxis> Site::siteAxis()
 {
-    parent_ = parent;
-    uniqueSiteIndex_ = uniqueSiteIndex;
-    molecule_ = std::move(molecule);
-    origin_ = origin;
+    return EnumOptions<Site::SiteAxis>("SiteAxis", {{Site::XAxis, "X"}, {Site::YAxis, "Y"}, {Site::ZAxis, "Z"}});
 }
 
 // Return the parent
@@ -35,36 +41,4 @@ std::shared_ptr<const Molecule> Site::molecule() const { return molecule_; }
 bool Site::hasAxes() const { return false; }
 
 // Return local axes
-const Matrix3 &Site::axes() const
-{
-    static Matrix3 dummy;
-    Messenger::warn("Returning empty axes for this Site, since it doesn't have any.\n");
-    return dummy;
-}
-
-/*
- * Oriented Site
- */
-
-OrientedSite::OrientedSite(const SpeciesSite *parent, std::optional<int> uniqueSiteIndex,
-                           std::shared_ptr<const Molecule> molecule, const Vec3<double> &origin, const Vec3<double> &xAxis,
-                           const Vec3<double> &yAxis, const Vec3<double> &zAxis)
-    : Site(parent, uniqueSiteIndex, std::move(molecule), origin)
-{
-    axes_.setColumn(0, xAxis);
-    axes_.setColumn(1, yAxis);
-    axes_.setColumn(2, zAxis);
-}
-
-// Return whether local axes are present
-bool OrientedSite::hasAxes() const { return true; }
-
-// Return enum options for SiteAxis
-EnumOptions<OrientedSite::SiteAxis> OrientedSite::siteAxis()
-{
-    return EnumOptions<OrientedSite::SiteAxis>(
-        "SiteAxis", {{OrientedSite::XAxis, "X"}, {OrientedSite::YAxis, "Y"}, {OrientedSite::ZAxis, "Z"}});
-}
-
-// Return local axes
-const Matrix3 &OrientedSite::axes() const { return axes_; }
+const Matrix3 &Site::axes() const { return axes_; }
diff --git a/src/classes/site.h b/src/classes/site.h
@@ -18,6 +18,8 @@ class Site
     public:
     Site(const SpeciesSite *parent = nullptr, std::optional<int> uniqueSiteIndex = {},
          std::shared_ptr<const Molecule> molecule = {}, const Vec3<double> &origin = {});
+    Site(const SpeciesSite *parent = nullptr, std::optional<int> uniqueSiteIndex = {},
+         std::shared_ptr<const Molecule> molecule = {}, const Matrix3 &axes = {}, const Vec3<double> &origin = {});
     ~Site() = default;
     Site &operator=(const Site &source) = default;
     Site(const Site &source) = default;
@@ -31,43 +33,14 @@ class Site
     const SpeciesSite *parent_;
     // Unique site index in the parent
     std::optional<int> uniqueSiteIndex_;
-    // Site origin
-    Vec3<double> origin_;
     // Molecule to which site is related (if relevant)
     std::shared_ptr<const Molecule> molecule_;
-
-    public:
-    // Return the parent
-    const SpeciesSite *parent() const;
-    // Return the unique site index in the parent
-    std::optional<int> uniqueSiteIndex() const;
-    // Return site origin
-    const Vec3<double> &origin() const;
-    // Return Molecule to which site is related (if relevant)
-    std::shared_ptr<const Molecule> molecule() const;
-    // Return whether local axes are present
-    virtual bool hasAxes() const;
-    // Return local axes
-    virtual const Matrix3 &axes() const;
-};
-
-// Oriented Site Definition
-class OrientedSite : public Site
-{
-    public:
-    OrientedSite(const SpeciesSite *parent = nullptr, std::optional<int> uniqueSiteIndex = {},
-                 std::shared_ptr<const Molecule> molecule = {}, const Vec3<double> &origin = {}, const Vec3<double> &xAxis = {},
-                 const Vec3<double> &yAxis = {}, const Vec3<double> &zAxis = {});
-    OrientedSite &operator=(const OrientedSite &source) = default;
-    OrientedSite(const OrientedSite &source) = default;
-    OrientedSite(OrientedSite &&source) = default;
-
-    /*
-     * Site Definition
-     */
-    private:
+    // Site origin
+    Vec3<double> origin_;
     // Local axes
     Matrix3 axes_;
+    // Whether local axes have been set / defined
+    bool hasAxes_{false};
 
     public:
     // Axis Enum
@@ -78,11 +51,21 @@ class OrientedSite : public Site
         ZAxis = 2
     };
     // Return enum options for SiteAxis
-    static EnumOptions<OrientedSite::SiteAxis> siteAxis();
+    static EnumOptions<Site::SiteAxis> siteAxis();
+
+    public:
+    // Return the parent
+    const SpeciesSite *parent() const;
+    // Return the unique site index in the parent
+    std::optional<int> uniqueSiteIndex() const;
+    // Return site origin
+    const Vec3<double> &origin() const;
+    // Return Molecule to which site is related (if relevant)
+    std::shared_ptr<const Molecule> molecule() const;
     // Return whether local axes are present
-    bool hasAxes() const override;
+    bool hasAxes() const;
     // Return local axes
-    const Matrix3 &axes() const override;
+    const Matrix3 &axes() const;
     // Rotate about axis
-    void rotate(double angle, OrientedSite::SiteAxis axis);
+    void rotate(double angle, Site::SiteAxis axis);
 };
diff --git a/src/classes/siteStack.cpp b/src/classes/siteStack.cpp
@@ -74,7 +74,6 @@ bool SiteStack::create(Configuration *cfg, const SpeciesSite *site)
     // Set new index and clear old arrays
     configurationIndex_ = configuration_->contentsVersion();
     sites_.clear();
-    orientedSites_.clear();
 
     const auto &instances = site->instances();
     auto *targetSpecies = site->parent();
@@ -83,10 +82,7 @@ bool SiteStack::create(Configuration *cfg, const SpeciesSite *site)
     if (sPop == 0)
         return true;
 
-    if (sitesHaveOrientation_)
-        orientedSites_.reserve(instances.size() * sPop);
-    else
-        sites_.reserve(instances.size() * sPop);
+    sites_.reserve(instances.size() * sPop);
 
     Vec3<double> origin, x, y;
     const auto *box = configuration_->box();
@@ -113,7 +109,7 @@ bool SiteStack::create(Configuration *cfg, const SpeciesSite *site)
                 y.orthogonalise(x);
                 y.normalise();
 
-                orientedSites_.emplace_back(speciesSite_, index, molecule, origin, x, y, x * y);
+                sites_.emplace_back(speciesSite_, index, molecule, Matrix3(x, y, x * y), origin);
             }
             else
                 sites_.emplace_back(speciesSite_, index, molecule, origin);
@@ -129,7 +125,7 @@ bool SiteStack::create(Configuration *cfg, const SpeciesSite *site)
  */
 
 // Return number of sites in the stack
-int SiteStack::nSites() const { return (sitesHaveOrientation_ ? orientedSites_.size() : sites_.size()); }
+int SiteStack::nSites() const { return sites_.size(); }
 
 // Return site with index specified
-const Site &SiteStack::site(int index) const { return (sitesHaveOrientation_ ? orientedSites_.at(index) : sites_.at(index)); }
+const Site &SiteStack::site(int index) const { return sites_.at(index); }
diff --git a/src/classes/siteStack.h b/src/classes/siteStack.h
@@ -56,10 +56,8 @@ class SiteStack
     bool sitesInMolecules_;
     // Whether the current stack contains local axes information
     bool sitesHaveOrientation_;
-    // Basic site array (if no local axes are defined)
+    // Site array
     std::vector<Site> sites_;
-    // Oriented site array (if local axes are defined)
-    std::vector<OrientedSite> orientedSites_;
 
     public:
     // Return number of sites in the stack

diff --git a/src/classes/speciesSite.cpp b/src/classes/speciesSite.cpp
@@ -492,7 +492,7 @@ std::vector<std::shared_ptr<Site>> SpeciesSite::createFromParent() const
             y.orthogonalise(x);
             y.normalise();
 
-            sites.push_back(std::make_shared<OrientedSite>(this, index, nullptr, origin, x, y, x * y));
+            sites.push_back(std::make_shared<Site>(this, index, nullptr, Matrix3(x, y, x * y), origin));
         }
         else
             sites.push_back(std::make_shared<Site>(this, index, nullptr, origin));

diff --git a/src/generator/rotateFragment.cpp b/src/generator/rotateFragment.cpp
@@ -21,7 +21,7 @@ RotateFragmentGeneratorNode::RotateFragmentGeneratorNode(std::shared_ptr<SelectG
     keywords_.add<NodeKeyword<SelectGeneratorNode>>("Site", "Site to be rotated", site_, this,
                                                     NodeTypeVector{NodeType::Select});
     keywords_.add<NodeValueKeyword>("Rotation", "Rotation to perform", rotation_, this);
-    keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("Axis", "Axis for rotation", axis_, OrientedSite::siteAxis());
+    keywords_.add<EnumOptionsKeyword<Site::SiteAxis>>("Axis", "Axis for rotation", axis_, Site::siteAxis());
 }
 
 /*
@@ -63,13 +63,13 @@ bool RotateFragmentGeneratorNode::execute(const GeneratorContext &generatorConte
     Matrix3 rotationMatrix;
     switch (axis_)
     {
-        case (OrientedSite::SiteAxis::XAxis):
+        case (Site::SiteAxis::XAxis):
             rotationMatrix.createRotationAxis(site.axes().columnAsVec3(0), rotation_.asDouble(), false);
             break;
-        case (OrientedSite::SiteAxis::YAxis):
+        case (Site::SiteAxis::YAxis):
             rotationMatrix.createRotationAxis(site.axes().columnAsVec3(1), rotation_.asDouble(), false);
             break;
-        case (OrientedSite::SiteAxis::ZAxis):
+        case (Site::SiteAxis::ZAxis):
             rotationMatrix.createRotationAxis(site.axes().columnAsVec3(2), rotation_.asDouble(), false);
             break;
     }

diff --git a/src/generator/rotateFragment.h b/src/generator/rotateFragment.h
@@ -28,7 +28,7 @@ class RotateFragmentGeneratorNode : public GeneratorNode
     // Rotation
     NodeValue rotation_{90.0};
     // Axis
-    OrientedSite::SiteAxis axis_{OrientedSite::SiteAxis::XAxis};
+    Site::SiteAxis axis_{Site::SiteAxis::XAxis};
 
     /*
      * Execute

diff --git a/src/modules/axisAngle/axisAngle.cpp b/src/modules/axisAngle/axisAngle.cpp
@@ -20,12 +20,10 @@ AxisAngleModule::AxisAngleModule() : Module(ModuleTypes::AxisAngle)
     keywords_.setOrganisation("Options", "Sites", "Specify sites defining the axis angle interaction A-B...C.");
     keywords_.add<SpeciesSiteVectorKeyword>("SiteA", "Specify site(s) which represent 'A' in the interaction A-B...C", a_,
                                             true);
-    keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("AxisA", "Axis to use from site A", axisA_,
-                                                              OrientedSite::siteAxis());
+    keywords_.add<EnumOptionsKeyword<Site::SiteAxis>>("AxisA", "Axis to use from site A", axisA_, Site::siteAxis());
     keywords_.add<SpeciesSiteVectorKeyword>("SiteB", "Specify site(s) which represent 'B' in the interaction A-B...C", b_,
                                             true);
-    keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("AxisB", "Axis to use from site B", axisB_,
-                                                              OrientedSite::siteAxis());
+    keywords_.add<EnumOptionsKeyword<Site::SiteAxis>>("AxisB", "Axis to use from site B", axisB_, Site::siteAxis());
 
     keywords_.setOrganisation("Options", "Ranges", "Ranges over which to bin quantities from the calculation.");
     keywords_.add<Vec3DoubleKeyword>("DistanceRange", "Range (min, max, binwidth) of distance binning", distanceRange_,

diff --git a/src/modules/axisAngle/axisAngle.h b/src/modules/axisAngle/axisAngle.h
@@ -35,7 +35,7 @@ class AxisAngleModule : public Module
     // Target SpeciesSite definitions
     std::vector<const SpeciesSite *> a_, b_;
     // Axes to use for sites
-    OrientedSite::SiteAxis axisA_{OrientedSite::SiteAxis::XAxis}, axisB_{OrientedSite::SiteAxis::XAxis};
+    Site::SiteAxis axisA_{Site::SiteAxis::XAxis}, axisB_{Site::SiteAxis::XAxis};
     // Export file and format for RDF
     Data1DExportFileFormat exportFileAndFormatRDF_;
     // Export file and format for AxisAngle

diff --git a/src/modules/orientedSDF/orientedSDF.cpp b/src/modules/orientedSDF/orientedSDF.cpp
@@ -21,12 +21,10 @@ OrientedSDFModule::OrientedSDFModule() : Module(ModuleTypes::OrientedSDF)
     keywords_.setOrganisation("Options", "Sites", "Specify the central (A) and surrounding sites (B).");
     keywords_.add<SpeciesSiteVectorKeyword>("SiteA", "Set the site(s) 'A' which are to represent the origin of the SDF", a_,
                                             true);
-    keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("AxisA", "Axis to use from site A", axisA_,
-                                                              OrientedSite::siteAxis());
+    keywords_.add<EnumOptionsKeyword<Site::SiteAxis>>("AxisA", "Axis to use from site A", axisA_, Site::siteAxis());
     keywords_.add<SpeciesSiteVectorKeyword>(
         "SiteB", "Set the site(s) 'B' for which the distribution around the origin site(s) 'A' should be calculated", b_);
-    keywords_.add<EnumOptionsKeyword<OrientedSite::SiteAxis>>("AxisB", "Axis to use from site B", axisB_,
-                                                              OrientedSite::siteAxis());
+    keywords_.add<EnumOptionsKeyword<Site::SiteAxis>>("AxisB", "Axis to use from site B", axisB_, Site::siteAxis());
 
     keywords_.setOrganisation("Options", "Ranges", "Ranges over which to bin quantities from the calculation.");
     keywords_.add<RangeKeyword>("AngleRange", "Axis angle range required to permit a site to be binned in the SDF",

diff --git a/src/modules/orientedSDF/orientedSDF.h b/src/modules/orientedSDF/orientedSDF.h
@@ -23,7 +23,7 @@ class OrientedSDFModule : public Module
     // Target SpeciesSite definitions
     std::vector<const SpeciesSite *> a_, b_;
     // Axes to use for sites
-    OrientedSite::SiteAxis axisA_{OrientedSite::SiteAxis::XAxis}, axisB_{OrientedSite::SiteAxis::XAxis};
+    Site::SiteAxis axisA_{Site::SiteAxis::XAxis}, axisB_{Site::SiteAxis::XAxis};
     // Whether to exclude correlations between sites on the same molecule
     bool excludeSameMolecule_{true};
     // Range along X axis

diff --git a/tests/procedure/rotateFragment.cpp b/tests/procedure/rotateFragment.cpp
@@ -61,7 +61,7 @@ TEST(RotateFragmentGeneratorNodeTest, Benzene)
     // Rotate Benzene around the Z-Axis of the site (which is defined at the COG, which is at the origin)
     auto &forEachB = select->branch()->get();
     auto rotate = forEachB.create<RotateFragmentGeneratorNode>("RotateBenzene", select);
-    rotate->keywords().setEnumeration("Axis", OrientedSite::SiteAxis::ZAxis);
+    rotate->keywords().setEnumeration("Axis", Site::SiteAxis::ZAxis);
 
     for (auto x = 90.0; x <= 360.0; x += 90.0)
     {